That's pretty much normal for these transmissions, just keep an eye on the gear oil when you drain it out, and check for excessive metal in the bottom of the drain pan .
I had the same problem with getting water into the transmission through the speedometer drive boot, this was back in the mid to late '80's, before I had heard of the inter net, let alone any BMW motorcycle groups .
Went on for 5 years, until I found out myself what was causing it, definitely damaged the bearings in the transmission, when I had the transmission overhauled about 2 years ago, I was given all of the old internal parts from the transmission, and you could see the rust damage on the ball bearings, and races .
Kind of explained the increasing amount of ferrous metal flakes when I drained the gear oil out of the bike .